Schrödinger 2013–1


This is the program version that is currently recommended by NSC.

Level of support

Tier 2 NSC has only limited experience with this software, but we will try to help as much as possible. We have ran some tests, for example, if the program comes with a test suite, but they may be far from exhaustive. We will try to install and test new versions, as soon as we can.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

How to run

You can submit jobs from the Maestro GUI, so the easiest way to get started is to start Maestro and then set up and submit your jobs from there.

Most of the Schrödinger products can also be run from the command line. Please contact NSC Support if you need help setting up a script for running jobs with one of the Schrödinger products.

Starting the Maestro GUI

When running the Maestro GUI (or any of the other variations of the GUI, such as BioLuminate, MaterialsScience, Jaguar, etc.) NSC recommends using ThinLinc to access Triolith.

For more information on how to use ThinLinc, please see: www.nsc.liu.se/systems/triolith/#accessing_triolith_thinlinc

Starting the GUI:

Start a terminal and execute the following on the command line:

$ module load schrodinger/2013-1-nsc
$ maestro

Example scripts for running Jaguar

Example batch script for running a Jaguar job on one compute node:

#!/bin/bash

#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --ntasks=16
#SBATCH --account=account-string

module load schrodinger/2013-1-nsc

export TMPDIR=$SNIC_TMP

jaguar run jobname.in -DEBUG -TPP 16 -WAIT
#END OF SCRIPT

Example batch script for running a Jaguar job across two compute nodes:

#!/bin/bash

#SBATCH --time=24:00:00
#SBATCH --nodes=2
#SBATCH --exclusive
#SBATCH --ntasks=32
#SBATCH --account=account-string

module load schrodinger/2013-1-nsc

SCRDIR=$SNIC_TMP
export SCHRODINGER_TMPDIR=${SCRDIR}

# Create hostfile
export SCHRODINGER_HOSTS=$SCRDIR/hostfile.txt
for node in $(hostlist -e $SLURM_JOB_NODELIST)
do
    echo "name: $node" >> $SCHRODINGER_HOSTS
    echo "schrodinger: $SCHRODINGER" >> $SCHRODINGER_HOSTS
    echo "tmpdir: $SCRDIR" >> $SCHRODINGER_HOSTS
    echo "processors: $SLURM_CPUS_ON_NODE" >> $SCHRODINGER_HOSTS
    echo "" >> $SCHRODINGER_HOSTS
done
echo "Using SCHRODINGER_HOSTS=$SCHRODINGER_HOSTS:"
cat $SCHRODINGER_HOSTS
echo

export TMPDIR=$SCRDIR
export SCHRODINGER_MPIRUN_OPTIONS="-x TMPDIR"

jaguar run jobname.in -DEBUG -OMPI 2 -TPP 16 -WAIT -HOST "$(hostlist -s " " -e $SLURM_JOB_NODELIST)"
#END OF SCRIPT

Note that you must edit the jobname and the account-string before submitting!

Available products

Product name Version
BIOLUMINATE 1.1
CANVAS 1.6
COMBIGLIDE 2.9
CONFGEN 2.4
CORE Hopping 1.3
EPIK 2.4
GLIDE 5.9
IMPACT 5.9
JAGUAR 8.0
KNIME 1.6
LIAISON 5.9
LIGPREP 2.6
MACROMODEL 10.0
MAESTRO 9.4
MAESTRO ELEMENTS 1.4
MCPRO+ 3.0
PHASE 3.5
PRIMEX 2.0
PRIME 3.2
QIKPROP 3.6
QSITE 5.9
SITEMAP 2.7
STRIKE 2.2

Disclaimer

NSC takes no responsibility for the correctness of results produced with the binaries! Hence, always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.